//
//  Copyright (C) 2002-2021 Greg Landrum and other RDKit contributors
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include "SmartsWrite.h"
#include <sstream>
#include <cstdint>
#include <boost/algorithm/string.hpp>
#include "SmilesWrite.h"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Canon.h>
#include <GraphMol/new_canon.h>
#include <RDGeneral/Exceptions.h>
#include <RDGeneral/RDLog.h>

namespace RDKit {
using namespace Canon;

// local utility namespace
namespace {

enum class QueryBoolFeatures {
  HAS_AND = 0x1,
  HAS_LOWAND = 0x2,
  HAS_OR = 0x4,
  HAS_RECURSION = 0x8
};

std::string _recurseGetSmarts(const QueryAtom *qatom,
                              const QueryAtom::QUERYATOM_QUERY *node,
                              bool negate, unsigned int &features,
                              const SmilesWriteParams &params);
std::string _recurseBondSmarts(const Bond *bond,
                               const QueryBond::QUERYBOND_QUERY *node,
                               bool negate, int atomToLeftIdx,
                               unsigned int &features,
                               const SmilesWriteParams &params);

std::string _combineChildSmarts(std::string cs1, unsigned int features1,
                                std::string cs2, unsigned int features2,
                                std::string descrip, unsigned int &features) {
  std::string res = "";
  if ((descrip.find("Or") > 0) && (descrip.find("Or") < descrip.length())) {
    // if either of child smarts already have a "," and ";" we can't have one
    // more OR here
    if ((features1 & static_cast<unsigned int>(QueryBoolFeatures::HAS_LOWAND) &&
         features1 & static_cast<unsigned int>(QueryBoolFeatures::HAS_OR)) ||
        (features2 & static_cast<unsigned int>(QueryBoolFeatures::HAS_LOWAND) &&
         features2 & static_cast<unsigned int>(QueryBoolFeatures::HAS_OR))) {
      throw ValueErrorException(
          "This is a non-smartable query - OR above and below AND in the "
          "binary tree");
    }
    res += cs1;
    if (!(cs1.empty() || cs2.empty())) {
      res += ",";
    }
    res += cs2;
    features |= static_cast<unsigned int>(QueryBoolFeatures::HAS_OR);
  } else if ((descrip.find("And") > 0) &&
             (descrip.find("And") < descrip.length())) {
    std::string symb;
    if (features1 & static_cast<unsigned int>(QueryBoolFeatures::HAS_OR) ||
        features2 & static_cast<unsigned int>(QueryBoolFeatures::HAS_OR)) {
      symb = ";";
      features |= static_cast<unsigned int>(QueryBoolFeatures::HAS_LOWAND);
    } else {
      symb = "&";
      features |= static_cast<unsigned int>(QueryBoolFeatures::HAS_AND);
    }
    res += cs1;
    if (!(cs1.empty() || cs2.empty())) {
      res += symb;
    }
    res += cs2;
  } else {
    std::stringstream err;
    err << "Don't know how to combine using " << descrip;
    throw ValueErrorException(err.str());
  }
  features |= features1;
  features |= features2;

  return res;
}  // namespace

template <typename T>
void describeQuery(const T *query, std::string leader = "\t") {
  // BOOST_LOG(rdInfoLog) << leader << query->getDescription() << std::endl;
  typename T::CHILD_VECT_CI iter;
  for (iter = query->beginChildren(); iter != query->endChildren(); ++iter) {
    describeQuery(iter->get(), leader + "\t");
  }
}

const static std::string _qatomHasStereoSet = "_qatomHasStereoSet";
std::string getAtomSmartsSimple(const QueryAtom *qatom,
                                const Atom::QUERYATOM_QUERY *query,
                                bool &needParen, bool checkForSymbol,
                                const SmilesWriteParams &) {
  PRECONDITION(query, "bad query");

  auto *equery = dynamic_cast<const ATOM_EQUALS_QUERY *>(query);

  std::string descrip = query->getDescription();
  bool hasVal = false;
  enum class Modifiers : std::uint8_t {
    NONE,
    RANGE,
    LESS,
    GREATER
  };
  Modifiers mods = Modifiers::NONE;
  if (boost::starts_with(descrip, "range_")) {
    mods = Modifiers::RANGE;
    descrip = descrip.substr(6);
  } else if (boost::starts_with(descrip, "less_")) {
    mods = Modifiers::LESS;
    descrip = descrip.substr(5);
  } else if (boost::starts_with(descrip, "greater_")) {
    mods = Modifiers::GREATER;
    descrip = descrip.substr(8);
  }
  std::stringstream res;
  if (descrip == "AtomImplicitHCount") {
    res << "h";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomHasImplicitH") {
    res << "h";
    needParen = true;
  } else if (descrip == "AtomTotalValence") {
    res << "v";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomAtomicNum") {
    if (!qatom->hasProp(common_properties::smilesSymbol)) {
      res << "#";
      hasVal = true;
      needParen = true;
    }
  } else if (descrip == "AtomExplicitDegree") {
    res << "D";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomNonHydrogenDegree") {
    res << "d";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomTotalDegree") {
    res << "X";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomHasRingBond") {
    res << "x";
    needParen = true;
  } else if (descrip == "AtomHCount") {
    res << "H";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomIsAliphatic") {
    res << "A";
    needParen = false;
  } else if (descrip == "AtomIsAromatic") {
    res << "a";
    needParen = false;
  } else if (descrip == "AtomNull") {
    res << "*";
    needParen = false;
  } else if (descrip == "AtomInRing") {
    res << "R";
    needParen = true;
  } else if (descrip == "AtomMinRingSize") {
    res << "r";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomInNRings") {
    res << "R";
    if (mods == Modifiers::NONE && equery && equery->getVal() >= 0) {
      hasVal = true;
    }
    needParen = true;
  } else if (descrip == "AtomHasHeteroatomNeighbors") {
    res << "z";
    needParen = true;
  } else if (descrip == "AtomNumHeteroatomNeighbors") {
    res << "z";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomHasAliphaticHeteroatomNeighbors") {
    res << "Z";
    needParen = true;
  } else if (descrip == "AtomNumAliphaticHeteroatomNeighbors") {
    res << "Z";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomFormalCharge") {
    int val = equery ? equery->getVal() : 0;

    if (val < 0) {
      res << "-";
    } else {
      res << "+";
    }
    if (mods == Modifiers::NONE && abs(val) != 1) {
      res << abs(val);
    }
    needParen = true;
  } else if (descrip == "AtomNegativeFormalCharge") {
    int val = equery ? equery->getVal() : 0;
    if (val < 0) {
      res << "+";
    } else {
      res << "-";
    }
    if (mods == Modifiers::NONE && abs(val) != 1) {
      res << abs(val);
    }
    needParen = true;
  } else if (descrip == "AtomHybridization" && equery) {
    res << "^";
    switch (equery->getVal()) {
      case Atom::S:
        res << "0";
        break;
      case Atom::SP:
        res << "1";
        break;
      case Atom::SP2:
        res << "2";
        break;
      case Atom::SP3:
        res << "3";
        break;
      case Atom::SP3D:
        res << "4";
        break;
      case Atom::SP3D2:
        res << "5";
        break;
    }
    needParen = true;
  } else if (descrip == "AtomMass" && equery) {
    res << equery->getVal() / massIntegerConversionFactor << "*";
    needParen = true;
  } else if (descrip == "AtomIsotope" && equery) {
    res << equery->getVal() << "*";
    needParen = true;
  } else if (descrip == "AtomRingBondCount") {
    res << "x";
    hasVal = true;
    needParen = true;
  } else if (descrip == "AtomUnsaturated") {
    res << "$(*=,:,#*)";
    needParen = true;
  } else if (descrip == "AtomType" && equery) {
    int atNum;
    bool isAromatic;
    parseAtomType(equery->getVal(), atNum, isAromatic);
    if (!checkForSymbol || !qatom->hasProp(common_properties::smilesSymbol)) {
      std::string symbol = PeriodicTable::getTable()->getElementSymbol(atNum);
      if (isAromatic) {
        symbol[0] += ('a' - 'A');
      }
      res << symbol;

      if (!SmilesWrite::inOrganicSubset(atNum)) {
        needParen = true;
      }
    } else {
      if (isAromatic) {
        res << "a";
      } else {
        res << "A";
      }
    }
  } else {
    BOOST_LOG(rdWarningLog)
        << "Cannot write SMARTS for query type : " << descrip
        << ". Ignoring it." << std::endl;
    res << "*";
  }

  if (mods != Modifiers::NONE) {
    res << "{";
    const ATOM_RANGE_QUERY *rquery = nullptr;
    switch (mods) {
      case Modifiers::LESS:
        res << equery->getVal() << "-";
        break;
      case Modifiers::RANGE:
        rquery = dynamic_cast<const ATOM_RANGE_QUERY *>(query);
        CHECK_INVARIANT(rquery, "query could not be converted to range query");
        res << ((const ATOM_RANGE_QUERY *)query)->getLower() << "-"
            << ((const ATOM_RANGE_QUERY *)query)->getUpper();
        break;
      case Modifiers::GREATER:
        res << "-" << equery->getVal();
        break;
      default:
        break;
    }
    res << "}";
  } else if (hasVal) {
    res << equery->getVal();
  }

  // handle atomic stereochemistry
  if (qatom->hasOwningMol() &&
      qatom->getOwningMol().hasProp(common_properties::_doIsoSmiles)) {
    if (qatom->getChiralTag() != Atom::CHI_UNSPECIFIED &&
        !qatom->hasProp(_qatomHasStereoSet) &&
        !qatom->hasProp(common_properties::_brokenChirality)) {
      qatom->setProp(_qatomHasStereoSet, 1);
      switch (qatom->getChiralTag()) {
        case Atom::CHI_TETRAHEDRAL_CW:
          res << "@@";
          needParen = true;
          break;
        case Atom::CHI_TETRAHEDRAL_CCW:
          res << "@";
          needParen = true;
          break;
        default:
          break;
      }
    }
  }

  return res.str();
}

std::string getRecursiveStructureQuerySmarts(
    const QueryAtom::QUERYATOM_QUERY *query, const SmilesWriteParams &params) {
  PRECONDITION(query, "bad query");
  PRECONDITION(query->getDescription() == "RecursiveStructure", "bad query");
  const auto *rquery = dynamic_cast<const RecursiveStructureQuery *>(query);
  PRECONDITION(rquery, "could not convert query to RecursiveStructureQuery");
  auto *qmol = const_cast<ROMol *>(rquery->getQueryMol());
  std::string res = MolToSmarts(*qmol, params);
  res = "$(" + res + ")";
  if (rquery->getNegation()) {
    res = "!" + res;
  }
  return res;
}

std::string getBasicBondRepr(Bond::BondType typ, Bond::BondDir dir,
                             bool reverseDative,
                             const SmilesWriteParams &params) {
  std::string res;
  switch (typ) {
    case Bond::SINGLE:
      res = "-";
      if (params.doIsomericSmiles) {
        if (dir == Bond::ENDDOWNRIGHT) {
          res = "\\";
        } else if (dir == Bond::ENDUPRIGHT) {
          res = "/";
        }
      }
      break;
    case Bond::DOUBLE:
      res = "=";
      break;
    case Bond::TRIPLE:
      res = "#";
      break;
    case Bond::QUADRUPLE:
      res = "$";
      break;
    case Bond::AROMATIC:
      res = ":";
      if (params.doIsomericSmiles) {
        if (dir == Bond::ENDDOWNRIGHT) {
          res = "\\";
        } else if (dir == Bond::ENDUPRIGHT) {
          res = "/";
        }
      }
      break;
    case Bond::DATIVE:
      if (params.includeDativeBonds) {
        if (reverseDative) {
          res = "<-";
        } else {
          res = "->";
        }
      } else {
        res = "-";
      }
      break;
    case Bond::ZERO:
      res = "~";  // Actually means "any", but we use ~ for unknown bond types
                  // in SMILES,
      break;      // and this will match a ZOB.
    default:
      res = "";
  }
  return res;
}  // namespace

std::string getBondSmartsSimple(const Bond *bond,
                                const QueryBond::QUERYBOND_QUERY *bquery,
                                int atomToLeftIdx,
                                const SmilesWriteParams &params) {
  PRECONDITION(bond, "bad bond");
  PRECONDITION(bquery, "bad query");

  auto *equery = dynamic_cast<const BOND_EQUALS_QUERY *>(bquery);

  std::string descrip = bquery->getDescription();
  std::string res = "";
  if (descrip == "BondNull") {
    res += "~";
  } else if (descrip == "BondInRing") {
    res += "@";
  } else if (descrip == "SingleOrAromaticBond") {
    auto dir = bond->getBondDir();
    switch (dir) {
      case Bond::ENDDOWNRIGHT: {
        res += "\\";
        break;
      }
      case Bond::ENDUPRIGHT: {
        res += "/";
        break;
      }
      default:
        break;
    }
  } else if (descrip == "SingleOrDoubleBond") {
    res += "-,=";
  } else if (descrip == "DoubleOrAromaticBond") {
    res += "=,:";
  } else if (descrip == "SingleOrDoubleOrAromaticBond") {
    res += "-,=,:";
  } else if (descrip == "BondDir" && equery) {
    int val = equery->getVal();
    if (val == static_cast<int>(Bond::ENDDOWNRIGHT)) {
      res += "\\";
    } else if (val == static_cast<int>(Bond::ENDUPRIGHT)) {
      res += "/";
    } else {
      throw "Can't write smarts for this bond dir type";
    }
  } else if (descrip == "BondOrder" && equery) {
    bool reverseDative =
        (atomToLeftIdx >= 0 &&
         bond->getBeginAtomIdx() != static_cast<unsigned int>(atomToLeftIdx));
    res += getBasicBondRepr(static_cast<Bond::BondType>(equery->getVal()),
                            bond->getBondDir(), reverseDative, params);
  } else {
    std::stringstream msg;
    msg << "Can't write smarts for this query bond type: " << descrip;
    throw msg.str().c_str();
  }
  return res;
}

std::string _recurseGetSmarts(const QueryAtom *qatom,
                              const QueryAtom::QUERYATOM_QUERY *node,
                              bool negate, unsigned int &features,
                              const SmilesWriteParams &params) {
  PRECONDITION(node, "bad node");
  // the algorithm goes something like this
  // - recursively get the smarts for the child queries
  // - combine the child smarts using the following rules:
  //      - if we are currently at an OR query, combine the subqueries with a
  //      ",",
  //        but only if neither of child smarts do not contain "," and ";"
  //        This situation leads to a no smartable situation and throw an
  //        error
  //      - if we are currently at an and query, combine the child smarts with
  //      "&"
  //        if neither of the child smarts contain a "," - otherwise combine
  //        them
  //        the child smarts with a ";"
  //
  // There is an additional complication with composite nodes that carry a
  // negation - in this
  // case we will propagate the negation to the child nodes using the
  // following rules
  //   NOT (a AND b) = ( NOT (a)) AND ( NOT (b))
  //   NOT (a OR b) = ( NOT (a)) OR ( NOT (b))

  auto descrip = node->getDescription();

  unsigned int child1Features = 0;
  unsigned int child2Features = 0;
  auto chi = node->beginChildren();
  auto child1 = chi->get();
  auto dsc1 = child1->getDescription();

  ++chi;
  CHECK_INVARIANT(chi != node->endChildren(),
                  "Not enough children on the query");

  bool needParen;
  std::string csmarts1;
  // deal with the first child
  if (dsc1 == "RecursiveStructure") {
    csmarts1 = getRecursiveStructureQuerySmarts(child1, params);
    features |= static_cast<unsigned int>(QueryBoolFeatures::HAS_RECURSION);
  } else if ((dsc1 != "AtomOr") && (dsc1 != "AtomAnd")) {
    // child 1 is a simple node, but we only check for the smilesSymbol
    //  if descrip=="AtomAnd"
    csmarts1 = getAtomSmartsSimple(qatom, child1, needParen,
                                   descrip == "AtomAnd", params);
    bool nneg = (negate) ^ (child1->getNegation());
    if (nneg) {
      csmarts1 = "!" + csmarts1;
    }
  } else {
    // child 1 is composite node - recurse
    bool nneg = (negate) ^ (child1->getNegation());
    csmarts1 = _recurseGetSmarts(qatom, child1, nneg, child1Features, params);
  }
  // ok if we have a negation and we have an OR , we have to change to
  // an AND since we propagated the negation
  // i.e NOT (A OR B) = (NOT (A)) AND (NOT(B))
  if (negate) {
    if (descrip == "AtomOr") {
      descrip = "AtomAnd";
    } else if (descrip == "AtomAnd") {
      descrip = "AtomOr";
    }
  }
  auto res = csmarts1;
  while (chi != node->endChildren()) {
    auto child2 = chi->get();
    ++chi;

    auto dsc2 = child2->getDescription();
    std::string csmarts2;

    // deal with the next child
    if (dsc2 == "RecursiveStructure") {
      csmarts2 = getRecursiveStructureQuerySmarts(child2, params);
      features |= static_cast<unsigned int>(QueryBoolFeatures::HAS_RECURSION);
    } else if ((dsc2 != "AtomOr") && (dsc2 != "AtomAnd")) {
      // child 2 is a simple node
      csmarts2 = getAtomSmartsSimple(qatom, child2, needParen, false, params);
      bool nneg = (negate) ^ (child2->getNegation());
      if (nneg) {
        csmarts2 = "!" + csmarts2;
      }
    } else {
      bool nneg = (negate) ^ (child2->getNegation());
      csmarts2 = _recurseGetSmarts(qatom, child2, nneg, child2Features, params);
    }

    res = _combineChildSmarts(res, child1Features, csmarts2, child2Features,
                              descrip, features);
  }
  return res;
}

std::string _recurseBondSmarts(const Bond *bond,
                               const QueryBond::QUERYBOND_QUERY *node,
                               bool negate, int atomToLeftIdx,
                               unsigned int &features,
                               const SmilesWriteParams &params) {
  // the algorithm goes something like this
  // - recursively get the smarts for the child query bonds
  // - combine the child smarts using the following rules:
  //      - if we are currently at an OR query, combine the subqueries with a
  //      ",",
  //        but only if neither of child smarts do not contain "," and ";"
  //        This situation leads to a no smartable situation and throw an
  //        error
  //      - if we are currently at an and query, combine the child smarts with
  //      "&"
  //        if neither of the child smarts contain a "," - otherwise combine
  //        them
  //        the child smarts with a ";"
  //
  // There is an additional complication with composite nodes that carry a
  // negation - in this
  // case we will propagate the negation to the child nodes using the
  // following rules
  //   NOT (a AND b) = ( NOT (a)) AND ( NOT (b))
  //   NOT (a OR b) = ( NOT (a)) OR ( NOT (b))
  PRECONDITION(bond, "bad bond");
  PRECONDITION(node, "bad node");
  std::string descrip = node->getDescription();
  std::string res = "";

  const QueryBond::QUERYBOND_QUERY *child1;
  const QueryBond::QUERYBOND_QUERY *child2;
  unsigned int child1Features = 0;
  unsigned int child2Features = 0;
  QueryBond::QUERYBOND_QUERY::CHILD_VECT_CI chi;

  chi = node->beginChildren();
  child1 = chi->get();
  chi++;
  child2 = chi->get();
  chi++;
  // OK we should be at the end of vector by now - since we can have only two
  // children,
  // well - at least in this case
  CHECK_INVARIANT(chi == node->endChildren(), "Too many children on the query");

  std::string dsc1, dsc2;
  dsc1 = child1->getDescription();
  dsc2 = child2->getDescription();
  std::string csmarts1, csmarts2;

  if ((dsc1 != "BondOr") && (dsc1 != "BondAnd")) {
    // child1 is  simple node get the smarts directly
    const auto *tchild = static_cast<const BOND_EQUALS_QUERY *>(child1);
    csmarts1 = getBondSmartsSimple(bond, tchild, atomToLeftIdx, params);
    bool nneg = (negate) ^ (tchild->getNegation());
    if (nneg) {
      csmarts1 = "!" + csmarts1;
    }
  } else {
    // child1 is a composite node recurse further
    bool nneg = (negate) ^ (child1->getNegation());
    csmarts1 = _recurseBondSmarts(bond, child1, nneg, atomToLeftIdx,
                                  child1Features, params);
  }

  // now deal with the second child
  if ((dsc2 != "BondOr") && (dsc2 != "BondAnd")) {
    // child 2 is a simple node
    const auto *tchild = static_cast<const BOND_EQUALS_QUERY *>(child2);
    csmarts2 = getBondSmartsSimple(bond, tchild, atomToLeftIdx, params);
    bool nneg = (negate) ^ (tchild->getNegation());
    if (nneg) {
      csmarts2 = "!" + csmarts2;
    }
  } else {
    // child two is a composite node - recurse
    bool nneg = (negate) ^ (child2->getNegation());
    csmarts1 = _recurseBondSmarts(bond, child2, nneg, atomToLeftIdx,
                                  child2Features, params);
  }

  // ok if we have a negation and we have to change the underlying logic,
  // since we propagated the negation i.e NOT (A OR B) = (NOT (A)) AND
  // (NOT(B))
  if (negate) {
    if (descrip == "BondOr") {
      descrip = "BondAnd";
    } else if (descrip == "BondAnd") {
      descrip = "BondOr";
    }
  }
  res += _combineChildSmarts(csmarts1, child1Features, csmarts2, child2Features,
                             descrip, features);
  return res;
}

std::string FragmentSmartsConstruct(
    ROMol &mol, unsigned int atomIdx, std::vector<Canon::AtomColors> &colors,
    UINT_VECT &ranks, const SmilesWriteParams &params,
    std::vector<unsigned int> &atomOrdering,
    std::vector<unsigned int> &bondOrdering,
    const boost::dynamic_bitset<> *bondsInPlay) {
  // this is dirty trick get around the fact that canonicalizeFragment
  // thinks we already called findSSSR - to do some atom ranking
  // but for smarts we are going to ignore that part. We will artificially
  // set the "SSSR" property to an empty property

  mol.getRingInfo()->reset();
  mol.getRingInfo()->initialize(FIND_RING_TYPE_SYMM_SSSR);
  for (auto &atom : mol.atoms()) {
    atom->updatePropertyCache(false);
  }

  // For Smarts, we avoid reordering of chiral atoms in canonicalizeFragment.
  bool doRandom = false;
  bool doChiralInversions = true;
  Canon::MolStack molStack;
  molStack.reserve(mol.getNumAtoms() + mol.getNumBonds());
  Canon::canonicalizeFragment(mol, atomIdx, colors, ranks, molStack,
                              bondsInPlay, nullptr, params.doIsomericSmiles,
                              doRandom, doChiralInversions);

  // now clear the "SSSR" property
  mol.getRingInfo()->reset();

  std::stringstream res;
  for (auto &msCI : molStack) {
    switch (msCI.type) {
      case Canon::MOL_STACK_ATOM: {
        auto *atm = msCI.obj.atom;
        res << SmartsWrite::GetAtomSmarts(atm, params);
        atomOrdering.push_back(atm->getIdx());
        break;
      }
      case Canon::MOL_STACK_BOND: {
        auto *bnd = msCI.obj.bond;
        res << SmartsWrite::GetBondSmarts(bnd, params, msCI.number);
        bondOrdering.push_back(bnd->getIdx());
        break;
      }
      case Canon::MOL_STACK_RING: {
        if (msCI.number < 10) {
          res << msCI.number;
        } else {
          res << "%" << msCI.number;
        }
        break;
      }
      case Canon::MOL_STACK_BRANCH_OPEN: {
        res << "(";
        break;
      }
      case Canon::MOL_STACK_BRANCH_CLOSE: {
        res << ")";
        break;
      }
      default:
        break;
    }
  }
  return res.str();
}

// this is the used when converting a SMILES or
// non-query atom from a mol file into SMARTS.
std::string getNonQueryAtomSmarts(const Atom *atom) {
  PRECONDITION(atom, "bad atom");
  PRECONDITION(!atom->hasQuery(), "atom should not have query");
  std::stringstream res;
  res << "[";

  int isotope = atom->getIsotope();
  if (isotope) {
    res << isotope;
  }

  std::string symbol;
  if (atom->getPropIfPresent(common_properties::smilesSymbol, symbol)) {
    res << symbol;
  } else if (SmilesWrite::inOrganicSubset(atom->getAtomicNum())) {
    res << "#" << atom->getAtomicNum();
  } else {
    res << atom->getSymbol();
  }
  bool addedChirality = false;
  if (atom->hasOwningMol() &&
      atom->getOwningMol().hasProp(common_properties::_doIsoSmiles)) {
    if (atom->getChiralTag() != Atom::CHI_UNSPECIFIED &&
        !atom->hasProp(_qatomHasStereoSet) &&
        !atom->hasProp(common_properties::_brokenChirality)) {
      atom->setProp(_qatomHasStereoSet, 1);
      switch (atom->getChiralTag()) {
        case Atom::CHI_TETRAHEDRAL_CW:
          res << "@@";
          addedChirality = true;
          break;
        case Atom::CHI_TETRAHEDRAL_CCW:
          res << "@";
          addedChirality = true;
          break;
        default:
          break;
      }
    }
  }

  if (addedChirality && atom->getNumExplicitHs() == 1) {
    // FIX: this isn't really correct in many cases, but
    //   fixing it requires opening a fairly large construction site on the
    //   SMARTS handling side. We'll do this later.
    res << "H";
  }
  auto chg = atom->getFormalCharge();
  if (chg) {
    if (chg == -1) {
      res << "-";
    } else if (chg == 1) {
      res << "+";
    } else if (chg < 0) {
      res << atom->getFormalCharge();
    } else {
      res << "+" << atom->getFormalCharge();
    }
  }
  int mapNum;
  if (atom->getPropIfPresent(common_properties::molAtomMapNumber, mapNum)) {
    res << ":";
    res << mapNum;
  }
  res << "]";
  return res.str();
}

// this is the used when converting a SMILES or
// non-query bond from a mol file into SMARTS.
std::string getNonQueryBondSmarts(const Bond *qbond, int atomToLeftIdx,
                                  const SmilesWriteParams &params) {
  PRECONDITION(qbond, "bad bond");
  std::string res;

  if (qbond->getIsAromatic()) {
    res = ":";
    if (params.doIsomericSmiles) {
      if (qbond->getBondDir() == Bond::ENDDOWNRIGHT) {
        res = "\\";
      } else if (qbond->getBondDir() == Bond::ENDUPRIGHT) {
        res = "/";
      }
    }

  } else {
    bool reverseDative =
        (atomToLeftIdx >= 0 &&
         qbond->getBeginAtomIdx() != static_cast<unsigned int>(atomToLeftIdx));
    res = getBasicBondRepr(qbond->getBondType(), qbond->getBondDir(),
                           reverseDative, params);
  }

  return res;
}

std::string molToSmarts(const ROMol &inmol, const SmilesWriteParams &params,
                        std::vector<AtomColors> &&colors,
                        const boost::dynamic_bitset<> *bondsInPlay) {
  PRECONDITION(params.rootedAtAtom < static_cast<int>(inmol.getNumAtoms()),
               "bad atom index");
  ROMol mol(inmol);
  const unsigned int nAtoms = mol.getNumAtoms();
  UINT_VECT ranks;
  ranks.reserve(nAtoms);
  // For smiles writing we would be canonicalizing but we will not do that
  // here. We will simply use the atom indices as the rank
  for (const auto &atom : mol.atoms()) {
    ranks.push_back(atom->getIdx());
  }

  if (params.doIsomericSmiles) {
    mol.setProp(common_properties::_doIsoSmiles, 1);
  }
  std::vector<unsigned int> atomOrdering;
  std::vector<unsigned int> bondOrdering;

  std::string res;
  auto colorIt = std::find(colors.begin(), colors.end(), Canon::WHITE_NODE);
  while (colorIt != colors.end()) {
    unsigned int nextAtomIdx = 0;
    std::string subSmi;

    if (params.rootedAtAtom > -1 &&
        colors[params.rootedAtAtom] == Canon::WHITE_NODE) {
      nextAtomIdx = params.rootedAtAtom;
    } else {
      // Try to find a non-chiral atom we have not processed yet.
      // If we can't find non-chiral atom, use the chiral atom with
      // the lowest rank (we are guaranteed to find an unprocessed atom).
      unsigned nextRank = nAtoms + 1;
      for (auto atom : mol.atoms()) {
        if (colors[atom->getIdx()] == Canon::WHITE_NODE) {
          if (atom->getChiralTag() != Atom::CHI_TETRAHEDRAL_CCW &&
              atom->getChiralTag() != Atom::CHI_TETRAHEDRAL_CW) {
            nextAtomIdx = atom->getIdx();
            break;
          }
          if (ranks[atom->getIdx()] < nextRank) {
            nextRank = ranks[atom->getIdx()];
            nextAtomIdx = atom->getIdx();
          }
        }
      }
    }

    subSmi = FragmentSmartsConstruct(mol, nextAtomIdx, colors, ranks, params,
                                     atomOrdering, bondOrdering, bondsInPlay);
    res += subSmi;

    colorIt = std::find(colors.begin(), colors.end(), Canon::WHITE_NODE);
    if (colorIt != colors.end()) {
      res += ".";
    }
  }
  inmol.setProp(common_properties::_smilesAtomOutputOrder, atomOrdering, true);
  inmol.setProp(common_properties::_smilesBondOutputOrder, bondOrdering, true);
  return res;
}

}  // namespace

namespace SmartsWrite {
std::string GetAtomSmarts(const Atom *atom, const SmilesWriteParams &params) {
  PRECONDITION(atom, "bad atom");
  std::string res;
  bool needParen = false;

  // BOOST_LOG(rdInfoLog)<<"Atom: " <<qatom->getIdx()<<std::endl;
  if (!atom->hasQuery()) {
    res = getNonQueryAtomSmarts(atom);
    // BOOST_LOG(rdInfoLog)<<"\tno query:" <<res;
    return res;
  }
  const auto query = atom->getQuery();
  PRECONDITION(query, "atom has no query");
  unsigned int queryFeatures = 0;
  std::string descrip = query->getDescription();
  if (descrip.empty()) {
    // we have simple atom - just generate the smiles and return
    res = SmilesWrite::GetAtomSmiles(atom);
    return res;
  } else {
    if ((descrip == "AtomOr") || (descrip == "AtomAnd")) {
      const QueryAtom *qatom = dynamic_cast<const QueryAtom *>(atom);
      PRECONDITION(qatom, "could not convert atom to query atom");
      // we have a composite query
      needParen = true;
      res = _recurseGetSmarts(qatom, query, query->getNegation(), queryFeatures,
                              params);
      if (res.length() == 1) {  // single atom symbol we don't need parens
        needParen = false;
      }
    } else if (descrip == "RecursiveStructure") {
      // it's a bare recursive structure query:
      res = getRecursiveStructureQuerySmarts(query, params);
      needParen = true;
    } else {  // we have a simple smarts
      const QueryAtom *qatom = dynamic_cast<const QueryAtom *>(atom);
      PRECONDITION(qatom, "could not convert atom to query atom");
      res = getAtomSmartsSimple(qatom, query, needParen, true, params);
      if (query->getNegation()) {
        res = "!" + res;
        needParen = true;
      }
    }
    std::string mapNum;
    if (atom->getPropIfPresent(common_properties::molAtomMapNumber, mapNum)) {
      needParen = true;
      res += ":" + mapNum;
    }
    std::string symbol;
    if (atom->getPropIfPresent(common_properties::smilesSymbol, symbol)) {
      needParen = true;
      if (!res.empty()) {
        res = symbol + ";" + res;
      } else {
        res = symbol;
      }
    }
    if (needParen) {
      res = "[" + res + "]";
    }
    return res;
  }
}

std::string GetBondSmarts(const Bond *bond, const SmilesWriteParams &params,
                          int atomToLeftIdx) {
  PRECONDITION(bond, "bad bond");

  std::string res = "";

  // BOOST_LOG(rdInfoLog) << "bond: " << bond->getIdx() << std::endl;
  ;
  // it is possible that we are regular single bond and we don't need to write
  // anything
  if (!bond->hasQuery()) {
    res = getNonQueryBondSmarts(bond, atomToLeftIdx, params);
    // BOOST_LOG(rdInfoLog) << "\tno query:" << res << std::endl;
    return res;
  }
  // describeQuery(bond->getQuery());
  auto qbond = dynamic_cast<const QueryBond *>(bond);
  if (!qbond && ((bond->getBondType() == Bond::SINGLE) ||
                 (bond->getBondType() == Bond::AROMATIC))) {
    BOOST_LOG(rdInfoLog) << "\tbasic:" << res << std::endl;
    return res;
  }
  CHECK_INVARIANT(qbond, "could not convert bond to QueryBond");

  const auto query = qbond->getQuery();
  CHECK_INVARIANT(query, "bond has no query");

  unsigned int queryFeatures = 0;
  auto descrip = query->getDescription();
  if ((descrip == "BondAnd") || (descrip == "BondOr")) {
    // composite query
    res = _recurseBondSmarts(bond, query, query->getNegation(), atomToLeftIdx,
                             queryFeatures, params);
  } else {
    // simple query
    if (query->getNegation()) {
      res = "!";
    }
    res += getBondSmartsSimple(bond, query, atomToLeftIdx, params);
  }
  // BOOST_LOG(rdInfoLog) << "\t  query:" << descrip << " " << res << std::endl;
  return res;
}

}  // end of namespace SmartsWrite

std::string MolToSmarts(const ROMol &mol, const SmilesWriteParams &ps) {
  const unsigned int nAtoms = mol.getNumAtoms();
  if (!nAtoms) {
    return "";
  }

  std::vector<AtomColors> colors(nAtoms, Canon::WHITE_NODE);
  return molToSmarts(mol, ps, std::move(colors), nullptr);
}

std::string MolFragmentToSmarts(const ROMol &mol,
                                const SmilesWriteParams &params,
                                const std::vector<int> &atomsToUse,
                                const std::vector<int> *bondsToUse) {
  PRECONDITION(!atomsToUse.empty(), "no atoms provided");
  PRECONDITION(!bondsToUse || !bondsToUse->empty(), "no bonds provided");

  auto nAtoms = mol.getNumAtoms();
  if (!nAtoms) {
    return "";
  }

  std::unique_ptr<boost::dynamic_bitset<>> bondsInPlay(nullptr);
  if (bondsToUse != nullptr) {
    bondsInPlay.reset(new boost::dynamic_bitset<>(mol.getNumBonds(), 0));
    for (auto bidx : *bondsToUse) {
      bondsInPlay->set(bidx);
    }
  }

  // Mark all atoms except the ones in atomIndices as already processed.
  // white: unprocessed
  // grey: partial
  // black: complete
  std::vector<AtomColors> colors(nAtoms, Canon::BLACK_NODE);
  for (const auto &idx : atomsToUse) {
    colors[idx] = Canon::WHITE_NODE;
  }

  SmilesWriteParams ps(params);
  ps.rootedAtAtom = -1;
  return molToSmarts(mol, ps, std::move(colors), bondsInPlay.get());
}

std::string MolToCXSmarts(const ROMol &mol, const SmilesWriteParams &params) {
  SmilesWriteParams ps(params);
  ps.includeDativeBonds = false;
  auto res = MolToSmarts(mol, ps);
  if (!res.empty()) {
    auto cxext = SmilesWrite::getCXExtensions(mol);
    if (!cxext.empty()) {
      res += " " + cxext;
    }
  }
  return res;
}

std::string MolFragmentToCXSmarts(const ROMol &mol,
                                  const SmilesWriteParams &params,
                                  const std::vector<int> &atomsToUse,
                                  const std::vector<int> *bondsToUse) {
  auto res = MolFragmentToSmarts(mol, params, atomsToUse, bondsToUse);
  if (!res.empty()) {
    auto cxext = SmilesWrite::getCXExtensions(mol);
    if (!cxext.empty()) {
      res += " " + cxext;
    }
  }
  return res;
}

}  // namespace RDKit
